.. AUTO-GENERATED FILE -- DO NOT EDIT!

nipype.interfaces.fsl.maths
===========================


:class:`ApplyMask`
------------------


Wraps command **fslmaths**

Use fslmaths to apply a binary mask to another image.

Inputs:: 

	[Mandatory]
	in_file : (an existing file name)
		image to operate on
	mask_file : (an existing file name)
		binary image defining mask space

	[Optional]
	args : (a string)
		Additional parameters to the command
	environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
		Environment variables
	ignore_exception : (a boolean)
		Print an error message instead of throwing an exception in case the interface fails to run
	internal_datatype : ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
		datatype to use for calculations (default is float)
	out_file : (a file name)
		image to write
	output_datatype : ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
		datatype to use for output (default uses input type)
	output_type : ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
		FSL output type


Outputs:: 

	out_file : (an existing file name)
		image written after calculations

:class:`ApplyMaskInput`
-----------------------






:class:`BinaryMaths`
--------------------


Wraps command **fslmaths**

Use fslmaths to perform mathematical operations using a second image or a numeric value.

Inputs:: 

	[Mandatory]
	in_file : (an existing file name)
		image to operate on
	operand_file : (an existing file name)
		second image to perform operation with
		exclusive: operand_value
	operand_value : (a float)
		value to perform operation with
		exclusive: operand_file
	operation : ('add' or 'sub' or 'mul' or 'div' or 'rem' or 'max' or 'min')
		operation to perform

	[Optional]
	args : (a string)
		Additional parameters to the command
	environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
		Environment variables
	ignore_exception : (a boolean)
		Print an error message instead of throwing an exception in case the interface fails to run
	internal_datatype : ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
		datatype to use for calculations (default is float)
	out_file : (a file name)
		image to write
	output_datatype : ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
		datatype to use for output (default uses input type)
	output_type : ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
		FSL output type


Outputs:: 

	out_file : (an existing file name)
		image written after calculations

:class:`BinaryMathsInput`
-------------------------






:class:`ChangeDataType`
-----------------------


Wraps command **fslmaths**

Use fslmaths to change the datatype of an image.

Inputs:: 

	[Mandatory]
	in_file : (an existing file name)
		image to operate on
	output_datatype : ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
		output data type

	[Optional]
	args : (a string)
		Additional parameters to the command
	environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
		Environment variables
	ignore_exception : (a boolean)
		Print an error message instead of throwing an exception in case the interface fails to run
	internal_datatype : ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
		datatype to use for calculations (default is float)
	out_file : (a file name)
		image to write
	output_type : ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
		FSL output type


Outputs:: 

	out_file : (an existing file name)
		image written after calculations

:class:`ChangeDataTypeInput`
----------------------------






:class:`DilateImage`
--------------------


Wraps command **fslmaths**

Use fslmaths to perform a spatial dilation of an image.

Inputs:: 

	[Mandatory]
	in_file : (an existing file name)
		image to operate on
	operation : ('mean' or 'modal' or 'max')
		filtering operation to perfoem in dilation

	[Optional]
	args : (a string)
		Additional parameters to the command
	environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
		Environment variables
	ignore_exception : (a boolean)
		Print an error message instead of throwing an exception in case the interface fails to run
	internal_datatype : ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
		datatype to use for calculations (default is float)
	kernel_file : (an existing file name)
		use external file for kernel
		exclusive: kernel_size
	kernel_shape : ('3D' or '2D' or 'box' or 'boxv' or 'gauss' or 'sphere' or 'file')
		kernel shape to use
	kernel_size : (a float)
		kernel size - voxels for box/boxv, mm for sphere, mm sigma for gauss
		exclusive: kernel_file
	out_file : (a file name)
		image to write
	output_datatype : ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
		datatype to use for output (default uses input type)
	output_type : ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
		FSL output type


Outputs:: 

	out_file : (an existing file name)
		image written after calculations

:class:`DilateInput`
--------------------






:class:`ErodeImage`
-------------------


Wraps command **fslmaths**

Use fslmaths to perform a spatial erosion of an image.

Inputs:: 

	[Mandatory]
	in_file : (an existing file name)
		image to operate on

	[Optional]
	args : (a string)
		Additional parameters to the command
	environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
		Environment variables
	ignore_exception : (a boolean)
		Print an error message instead of throwing an exception in case the interface fails to run
	internal_datatype : ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
		datatype to use for calculations (default is float)
	kernel_file : (an existing file name)
		use external file for kernel
		exclusive: kernel_size
	kernel_shape : ('3D' or '2D' or 'box' or 'boxv' or 'gauss' or 'sphere' or 'file')
		kernel shape to use
	kernel_size : (a float)
		kernel size - voxels for box/boxv, mm for sphere, mm sigma for gauss
		exclusive: kernel_file
	minimum_filter : (a boolean)
		if true, minimum filter rather than erosion by zeroing-out
	out_file : (a file name)
		image to write
	output_datatype : ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
		datatype to use for output (default uses input type)
	output_type : ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
		FSL output type


Outputs:: 

	out_file : (an existing file name)
		image written after calculations

:class:`ErodeInput`
-------------------






:class:`IsotropicSmooth`
------------------------


Wraps command **fslmaths**

Use fslmaths to spatially smooth an image with a gaussian kernel.

Inputs:: 

	[Mandatory]
	fwhm : (a float)
		fwhm of smoothing kernel
		exclusive: sigma
	in_file : (an existing file name)
		image to operate on
	sigma : (a float)
		sigma of smoothing kernel
		exclusive: fwhm

	[Optional]
	args : (a string)
		Additional parameters to the command
	environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
		Environment variables
	ignore_exception : (a boolean)
		Print an error message instead of throwing an exception in case the interface fails to run
	internal_datatype : ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
		datatype to use for calculations (default is float)
	out_file : (a file name)
		image to write
	output_datatype : ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
		datatype to use for output (default uses input type)
	output_type : ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
		FSL output type


Outputs:: 

	out_file : (an existing file name)
		image written after calculations

:class:`IsotropicSmoothInput`
-----------------------------






:class:`KernelInput`
--------------------






:class:`MathsCommand`
---------------------


Wraps command **fslmaths**



Inputs:: 

	[Mandatory]
	in_file : (an existing file name)
		image to operate on

	[Optional]
	args : (a string)
		Additional parameters to the command
	environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
		Environment variables
	ignore_exception : (a boolean)
		Print an error message instead of throwing an exception in case the interface fails to run
	internal_datatype : ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
		datatype to use for calculations (default is float)
	out_file : (a file name)
		image to write
	output_datatype : ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
		datatype to use for output (default uses input type)
	output_type : ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
		FSL output type


Outputs:: 

	out_file : (an existing file name)
		image written after calculations

:class:`MathsInput`
-------------------






:class:`MathsOutput`
--------------------






:class:`MeanImage`
------------------


Wraps command **fslmaths**

Use fslmaths to generate a mean image across a given dimension.

Inputs:: 

	[Mandatory]
	in_file : (an existing file name)
		image to operate on

	[Optional]
	args : (a string)
		Additional parameters to the command
	dimension : ('T' or 'X' or 'Y' or 'Z')
		dimension to mean across
	environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
		Environment variables
	ignore_exception : (a boolean)
		Print an error message instead of throwing an exception in case the interface fails to run
	internal_datatype : ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
		datatype to use for calculations (default is float)
	out_file : (a file name)
		image to write
	output_datatype : ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
		datatype to use for output (default uses input type)
	output_type : ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
		FSL output type


Outputs:: 

	out_file : (an existing file name)
		image written after calculations

:class:`MeanImageInput`
-----------------------






:class:`MultiImageMaths`
------------------------


Wraps command **fslmaths**

Use fslmaths to perform a sequence of mathematical operations.

Examples
~~~~~~~~
from nipype.interfaces.fsl import MultiImageMaths
maths = MultiImageMaths()
maths.inputs.in_file = "functional.nii"
maths.inputs.op_string = "-add %s -mul -1 -div %s"
maths.inputs.operand_files = ["functional2.nii", "functional3.nii"]
maths.inputs.out_file = functional4.nii
maths.cmdline
fslmaths functional1.nii -add functional2.nii -mul -1 -div functional3.nii functional4.nii

Inputs:: 

	[Mandatory]
	in_file : (an existing file name)
		image to operate on
	op_string : (a string)
		python formatted string of operations to perform
	operand_files : (an existing file name)
		list of file names to plug into op string

	[Optional]
	args : (a string)
		Additional parameters to the command
	environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
		Environment variables
	ignore_exception : (a boolean)
		Print an error message instead of throwing an exception in case the interface fails to run
	internal_datatype : ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
		datatype to use for calculations (default is float)
	out_file : (a file name)
		image to write
	output_datatype : ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
		datatype to use for output (default uses input type)
	output_type : ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
		FSL output type


Outputs:: 

	out_file : (an existing file name)
		image written after calculations

:class:`MultiImageMathsInput`
-----------------------------






:class:`SpatialFilter`
----------------------


Wraps command **fslmaths**

Use fslmaths to spatially filter an image.

Inputs:: 

	[Mandatory]
	in_file : (an existing file name)
		image to operate on
	operation : ('mean' or 'median' or 'meanu')
		operation to filter with

	[Optional]
	args : (a string)
		Additional parameters to the command
	environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
		Environment variables
	ignore_exception : (a boolean)
		Print an error message instead of throwing an exception in case the interface fails to run
	internal_datatype : ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
		datatype to use for calculations (default is float)
	kernel_file : (an existing file name)
		use external file for kernel
		exclusive: kernel_size
	kernel_shape : ('3D' or '2D' or 'box' or 'boxv' or 'gauss' or 'sphere' or 'file')
		kernel shape to use
	kernel_size : (a float)
		kernel size - voxels for box/boxv, mm for sphere, mm sigma for gauss
		exclusive: kernel_file
	out_file : (a file name)
		image to write
	output_datatype : ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
		datatype to use for output (default uses input type)
	output_type : ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
		FSL output type


Outputs:: 

	out_file : (an existing file name)
		image written after calculations

:class:`SpatialFilterInput`
---------------------------






:class:`TemporalFilter`
-----------------------


Wraps command **fslmaths**

Use fslmaths to apply a low, high, or bandpass temporal filter to a timeseries.

Inputs:: 

	[Mandatory]
	in_file : (an existing file name)
		image to operate on

	[Optional]
	args : (a string)
		Additional parameters to the command
	environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
		Environment variables
	highpass_sigma : (a float)
		highpass filter sigma (in volumes)
	ignore_exception : (a boolean)
		Print an error message instead of throwing an exception in case the interface fails to run
	internal_datatype : ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
		datatype to use for calculations (default is float)
	lowpass_sigma : (a float)
		lowpass filter sigma (in volumes)
	out_file : (a file name)
		image to write
	output_datatype : ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
		datatype to use for output (default uses input type)
	output_type : ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
		FSL output type


Outputs:: 

	out_file : (an existing file name)
		image written after calculations

:class:`TemporalFilterInput`
----------------------------






:class:`Threshold`
------------------


Wraps command **fslmaths**

Use fslmaths to apply a threshold to an image in a variety of ways.

Inputs:: 

	[Mandatory]
	in_file : (an existing file name)
		image to operate on
	thresh : (a float)
		threshold value

	[Optional]
	args : (a string)
		Additional parameters to the command
	direction : ('below' or 'above')
		zero-out either below or above thresh value
	environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
		Environment variables
	ignore_exception : (a boolean)
		Print an error message instead of throwing an exception in case the interface fails to run
	internal_datatype : ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
		datatype to use for calculations (default is float)
	out_file : (a file name)
		image to write
	output_datatype : ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
		datatype to use for output (default uses input type)
	output_type : ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
		FSL output type
	use_nonzero_voxels : (a boolean)
		use nonzero voxels to caluclate robust range
		requires: use_robust_range
	use_robust_range : (a boolean)
		inteperet thresh as percentage (0-100) of robust range


Outputs:: 

	out_file : (an existing file name)
		image written after calculations

:class:`UnaryMaths`
-------------------


Wraps command **fslmaths**

Use fslmaths to perorm a variety of mathematical operations on an image.

Inputs:: 

	[Mandatory]
	in_file : (an existing file name)
		image to operate on
	operation : ('exp' or 'log' or 'sin' or 'cos' or 'sqr' or 'sqrt' or 'recip' or 'abs' or 'bin' or 'index')
		operation to perform

	[Optional]
	args : (a string)
		Additional parameters to the command
	environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
		Environment variables
	ignore_exception : (a boolean)
		Print an error message instead of throwing an exception in case the interface fails to run
	internal_datatype : ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
		datatype to use for calculations (default is float)
	out_file : (a file name)
		image to write
	output_datatype : ('float' or 'char' or 'int' or 'short' or 'double' or 'input')
		datatype to use for output (default uses input type)
	output_type : ('NIFTI_PAIR' or 'NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI')
		FSL output type


Outputs:: 

	out_file : (an existing file name)
		image written after calculations

:class:`UnaryMathsInput`
------------------------





